NPLB13001U Plant Genomics
BSc Programme in Biology-Biotechnology
BSc Programme in Biology
This course is an advanced course in theoretical and applied genomics with a focus on plant technology and examples.
The key techniques used in molecular genetics and tools for analyzing data, from genomics to phenotyping, will be presented and examples both from model and crop plants are included. Together with these techniques the basis for the development of markers and how markers are used in molecular breeding is central. For an introduction a crash course in bioinformatics is included. The course will give information and give the students tools to describe and characterize genomes.
Following topics are covered:
Crash course, Bioinformatics and Crash course, Molecular genetics
Genomes: Model plants versus crops
Next-generation sequencing technologies
Transcription factors, focus on MYB family
Forward and reverse genetics
Genetic markers and Quantitative Trait Loci
Genotype – Phenotype
Map based cloning and QTL dissection
Biomarkers and RNAi/siRNA
There will be student workshop on four functional genomics assignments and the findings of the case study will be debated.
In practical exercises complementing the lectures, you will get familiar with some of the tools used, e.g. tracking of gene expression, both quantitatively as well as in plant tissue, analysis of quantitative trait loci, and genetic manipulation techniques.
After successful completion of the course, the students will
- Describe basic principles for the study of major model plants and general plant evolution
- Identify and describe the key techniques used for molecular genetics and selected tools used to analyse genomic information, including map based cloning and QTLs.
- Explain genetic markers and their use for qualitative and quantitative traits
- Compare basic central experimental techniques used in plant genomics and molecular breeding and propose their application for novel challenges
- Complete with confidence an assessment of the techniques used to study complex biological processes in plant model systems
- Apply common bioinformatic tools to screen databases of model plant species and use genome browsers to analyse simple problems
- Practice molecular and genetic tools for plant improvement through molecular breeding of crops for food, fodder and production of high value crops for e.g. biomedicine, biofuel and green factories
- Conduct a simple transformation procedure
- Evaluate various forward and reverse genomics approaches for gene isolation and functional studies
- Relate gene differences with phenotype by means of genomics
- Explain advantages or disadvantages of model plants versus crops
- Communicate effectively with other students in a debate to justify conclusions on a given problem
Laboratory manuals and a dedicated Plant Genomics Compendium, consisting of all relevant chapters and papers discussed in class will be distributed in electronic form. Next to the compendium, no specific textbook will be required for this course. However, general botany and genetics textbooks may be consulted for the most basic concepts not covered within this course. The student should on his or her own initiative locate additional reading material that matches lecture material.
Further information will be available on Absalon.
- Practical exercises
- Theory exercises
Written feedback is given for the reports.
- 7,5 ECTS
- Type of assessment
- Oral examinationOral examination (presentation and questions):
The students receive the assignment at 9.00 and submit an individual, short PowerPoint presentation at 12.00 the next day. The exact date is given in the beginning of the course. At the oral exam the student present the results of the assignment (5 min) followed by a short discussion of the course curriculum (15 min).
- Exam registration requirements
Three passed lab reports (75 %) and participation in the oral presentation of case are a requirement
- All aids allowed
- Marking scale
- 7-point grading scale
- Censorship form
- No external censorship
One internal examinator
The lab reports must be handed in two weeks before the re-examination (75% must be approved). Oral examination.
Criteria for exam assesment
See learning outcome.